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[ccp4bb] Re :Re: [ccp4bb] MAD phasing |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re :Re: MAD phasing From: Ethayathulla Abdulsamath ethaya_aiims {- at -} REDIFFMAIL {- dot -} COM Date: 2009-05-21 hello peteri tried phenix.autosol. It gave me following results. but the data analyses says that my data pseudo translational symmetry, I have pasted it. Do phenix handle pseudotranslation. Need suggestion on thisSolution # 1 BAYES-CC: 15.3 +/- 27.3 Dataset #1 SG: "P 61 2 2" FOM: 0.4Score type: SKEW CORR_RMSRaw scores: 0.04 0.67100x EST OF CC: 18.93 15.24 Refined heavy atom sites (fractional): xyz 0.865 0.471 0.070 xyz 0.099 0.513 0.070 Twinning and intensity statistics summary (acentric data):Statistics independent of twin laws - <I^2>/<I>^2 : 2.545 - <F>^2/<F^2> : 0.718 - < E^2-1 > : 0.852 - < L >! ;, <L^2>: 0.530, 0.370 Multivariate Z score L-test: 4.008 The multivariate Z score is a quality measure of the given spread in intensities. Good to reasonable data are expected to have a Z score lower than 3.5. Large values can indicate twinning, but small values do not necessarily exclude it.Statistics depending on twin laws------------------------------------------------------------------ Operator type R obs. Britton alpha H alpha ML alpha ------------------------------------------------------------------ h,-h-k,-l M 0.032 0.455 0.470 0.478 ------------------------------------------------------------------Patterson analyses&! nbsp; - Largest peak height : 61.921 (correspo nding p value : 1.218e-05)The analyses of the Patterson function reveals a significant off-origin peak that is 61.92 % of the origin peak, indicating pseudo translational symmetry. The chance of finding a peak of this or larger height by random in a structure without pseudo translational symmetry is equal to the 1.2181e-05. The detected tranlational NCS is most likely also responsible for the elevated intensity ratio. See the relevant section of the logfile for more details. The results of the L-test indicate that the intensity statistics Show more centric character than is expected for acentric data. This behavoir might be explained by the presence of the detected pseudo translation.+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++Thank youEthayathullaOn Thu, 21 May 2009 16:34:28 -0700 Peter Zwart wrote Did you check for twinning? Why don't you try to use phenix.autosol alone? P 2009/5/21 Ethayathulla Abdulsamath : > hello > > ! I am have a MAD dataset collected upto 2.3A but anomalous signal is upto > 3.5A. The dataset is in P6 and based on pointless and absences it is P6122. > Overall Rlin/rsym is (0.07/ 0.06). the overall redundancy is 10. I have two > Se peaks, i used solve/resolve to find those peaks. I used datasets from 3.5 > to 20A to find peaks i got two good peaks of occ (1.4 & 0.92). I did > analyze_solve and refined those peaks. Then i tried resolve to autobuild and > phasing but it didnt work. The r-factor FC vs FP is 0.40 and FOM 0.6, > although the results looks promising i couldnt find proper phasing using > phenix, resolve.autobuild. i tried phenix.autosol also but it didnt work. > how can i check the peaks are real. can anybody suggest me how do I proceed > further and what r the mistakes i am doing.. > > Thank you > Ethayathulla > FROM SOLVE > Site x &! nbsp; y z & nbsp; occ B -- PEAK HEIGHT -- > 1 0.386 0.986 0.050 1.449 60.000 23.82 > 2 0.623 0.997 0.046 0.921 60.000 22.11 > Summary of scoring for this solution: > -- over many solutions-- -- this solution -- > Criteria MEAN SD ! ; VALUE > Z-SCORE > Pattersons: 0.129 0.500 0.279 0.299 > Cross-validation Fourier: 4.83 2.62 41.8 14.1 > NatFourier CCx100: 3.28 1.24 3.93 0.521 > Mean figure of meritx100: 0.00 7.16 53.5 ! 7.48 > Correction for Z-scores: -10.5 > > Overall Z-score value: 11.9 > > > RESOLVE results > > CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.61 * > * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.39 * > * ESTIMATED FRACTION OF PHASE INFORMATION ! FROM MAP: 0.61 * > * NOTE: The fraction from prior will be roughly proportional to * > Overall average CC: 0.5423778 > Results of wilson scaling of model Fc to Fo : > Scale on I to apply to Fc = 1.934 > B-value to apply to Fc= 1.971 > Overall R-factor for FC vs FP: 0.404 for 3288 reflections > Leaving out 1 reflections with FC=0 and correcting R-factor to > 0.4036375 > from 0.4035717 as only 99.96960 % of the reflections are ok > Writing overall R-factor 0.4036375 to "resolve.rfactor" >! > > > > > > > > ##################### ############################## > A.S.Ethayathulla,Ph.D. > Department of Biophysics > All India Institute of Medical Sciences > Ansari Nagar > New Delhi-110029 > India. > ################################################### > > -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net ----------------------------------------------------------------- ################################################### A.S.Ethayathulla,Ph.D. Department of Biophysics All India Institute of Medical Sciences Ansari Nagar New Delhi-110029 India. ################################################### CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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